Calcium in PDB 1yo8: Structure of the C-Terminal Domain of Human Thrombospondin-2
Protein crystallography data
The structure of Structure of the C-Terminal Domain of Human Thrombospondin-2, PDB code: 1yo8
was solved by
C.B.Carlson,
D.A.Bernstein,
D.S.Annis,
T.M.Misenheimer,
B.A.Hannah,
D.F.Mosher,
J.L.Keck,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.60
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.437,
121.588,
155.330,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.8 /
28.4
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Binding sites:
The binding sites of Calcium atom in the Structure of the C-Terminal Domain of Human Thrombospondin-2
(pdb code 1yo8). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 30 binding sites of Calcium where determined in the
Structure of the C-Terminal Domain of Human Thrombospondin-2, PDB code: 1yo8:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 30 in 1yo8
Go back to
Calcium Binding Sites List in 1yo8
Calcium binding site 1 out
of 30 in the Structure of the C-Terminal Domain of Human Thrombospondin-2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of the C-Terminal Domain of Human Thrombospondin-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1182
b:46.9
occ:1.00
|
O
|
A:CYS948
|
2.3
|
49.5
|
1.0
|
O
|
A:ILE954
|
2.3
|
51.7
|
1.0
|
OD2
|
A:ASP939
|
2.3
|
51.2
|
1.0
|
O
|
A:ASN951
|
2.3
|
50.7
|
1.0
|
OD2
|
A:ASP937
|
2.3
|
50.2
|
1.0
|
OD2
|
A:ASP946
|
2.4
|
46.3
|
1.0
|
OD1
|
A:ASP946
|
2.6
|
46.2
|
1.0
|
OG
|
A:SER955
|
2.8
|
54.9
|
1.0
|
CG
|
A:ASP946
|
2.9
|
47.1
|
1.0
|
C
|
A:CYS948
|
3.3
|
49.8
|
1.0
|
C
|
A:ILE954
|
3.4
|
51.2
|
1.0
|
C
|
A:ASN951
|
3.4
|
51.6
|
1.0
|
CG
|
A:ASP937
|
3.4
|
52.3
|
1.0
|
CG
|
A:ASP939
|
3.5
|
52.0
|
1.0
|
OD1
|
A:ASP937
|
3.8
|
51.2
|
1.0
|
CB
|
A:SER955
|
3.9
|
53.7
|
1.0
|
CA
|
A:SER955
|
4.0
|
53.0
|
1.0
|
OD1
|
A:ASP939
|
4.0
|
51.6
|
1.0
|
N
|
A:SER955
|
4.1
|
52.0
|
1.0
|
N
|
A:PRO949
|
4.2
|
50.1
|
1.0
|
CA
|
A:CYS948
|
4.2
|
49.3
|
1.0
|
CB
|
A:CYS948
|
4.2
|
49.1
|
1.0
|
N
|
A:ASN952
|
4.2
|
52.0
|
1.0
|
CA
|
A:ASN952
|
4.2
|
53.2
|
1.0
|
N
|
A:ASN951
|
4.2
|
51.4
|
1.0
|
CA
|
A:CA1183
|
4.2
|
50.2
|
1.0
|
CA
|
A:PRO949
|
4.3
|
51.2
|
1.0
|
CA
|
A:ASN951
|
4.3
|
51.5
|
1.0
|
N
|
A:ILE954
|
4.3
|
50.6
|
1.0
|
CB
|
A:ASP946
|
4.4
|
49.0
|
1.0
|
CA
|
A:ILE954
|
4.4
|
50.1
|
1.0
|
N
|
A:CYS948
|
4.4
|
48.5
|
1.0
|
C
|
A:PRO949
|
4.6
|
52.1
|
1.0
|
C
|
A:ASN952
|
4.6
|
52.7
|
1.0
|
CB
|
A:ASP937
|
4.7
|
54.3
|
1.0
|
CB
|
A:ASP939
|
4.7
|
52.0
|
1.0
|
CB
|
A:ASN951
|
4.8
|
50.6
|
1.0
|
O
|
A:HOH1266
|
4.8
|
51.5
|
1.0
|
O
|
A:HOH1224
|
4.9
|
41.6
|
1.0
|
O
|
A:PRO949
|
4.9
|
53.3
|
1.0
|
N
|
A:GLU950
|
5.0
|
52.2
|
1.0
|
|
Calcium binding site 2 out
of 30 in 1yo8
Go back to
Calcium Binding Sites List in 1yo8
Calcium binding site 2 out
of 30 in the Structure of the C-Terminal Domain of Human Thrombospondin-2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of the C-Terminal Domain of Human Thrombospondin-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1183
b:50.2
occ:1.00
|
O
|
A:ILE941
|
2.2
|
55.6
|
1.0
|
O
|
A:HOH1266
|
2.3
|
51.5
|
1.0
|
OD1
|
A:ASP939
|
2.3
|
51.6
|
1.0
|
OD1
|
A:ASP935
|
2.3
|
58.5
|
1.0
|
OD1
|
A:ASP937
|
2.3
|
51.2
|
1.0
|
OD2
|
A:ASP946
|
2.5
|
46.3
|
1.0
|
CG
|
A:ASP939
|
3.3
|
52.0
|
1.0
|
CG
|
A:ASP937
|
3.4
|
52.3
|
1.0
|
C
|
A:ILE941
|
3.4
|
55.7
|
1.0
|
CG
|
A:ASP935
|
3.5
|
60.3
|
1.0
|
CG
|
A:ASP946
|
3.5
|
47.1
|
1.0
|
OD2
|
A:ASP939
|
3.6
|
51.2
|
1.0
|
OD2
|
A:ASP937
|
3.7
|
50.2
|
1.0
|
CB
|
A:ASP946
|
3.9
|
49.0
|
1.0
|
N
|
A:ILE941
|
4.1
|
55.5
|
1.0
|
CA
|
A:ILE941
|
4.1
|
55.2
|
1.0
|
N
|
A:ASP939
|
4.2
|
54.3
|
1.0
|
CA
|
A:CA1182
|
4.2
|
46.9
|
1.0
|
CA
|
A:ASP935
|
4.3
|
60.2
|
1.0
|
OD2
|
A:ASP935
|
4.3
|
61.9
|
1.0
|
CB
|
A:ILE941
|
4.3
|
54.7
|
1.0
|
C
|
A:PRO942
|
4.4
|
55.2
|
1.0
|
CB
|
A:ASP935
|
4.4
|
60.4
|
1.0
|
N
|
A:PRO942
|
4.4
|
56.1
|
1.0
|
N
|
A:ASP937
|
4.5
|
55.9
|
1.0
|
C
|
A:ASP935
|
4.5
|
59.5
|
1.0
|
N
|
A:ASP943
|
4.5
|
55.1
|
1.0
|
N
|
A:ASN938
|
4.5
|
55.3
|
1.0
|
CB
|
A:ASP939
|
4.6
|
52.0
|
1.0
|
O
|
A:PRO942
|
4.6
|
54.3
|
1.0
|
OD1
|
A:ASP946
|
4.6
|
46.2
|
1.0
|
O
|
A:PRO949
|
4.6
|
53.3
|
1.0
|
CA
|
A:PRO942
|
4.6
|
56.1
|
1.0
|
OD1
|
A:ASP943
|
4.7
|
56.4
|
1.0
|
CB
|
A:ASP937
|
4.7
|
54.3
|
1.0
|
CA
|
A:PRO949
|
4.7
|
51.2
|
1.0
|
N
|
A:ASN940
|
4.7
|
54.7
|
1.0
|
OG
|
A:SER955
|
4.8
|
54.9
|
1.0
|
CA
|
A:ASP939
|
4.8
|
53.4
|
1.0
|
N
|
A:PHE936
|
4.8
|
58.5
|
1.0
|
O
|
A:ASP935
|
4.8
|
59.0
|
1.0
|
C
|
A:ASP937
|
4.9
|
54.8
|
1.0
|
CA
|
A:ASP937
|
4.9
|
54.9
|
1.0
|
C
|
A:ASP939
|
4.9
|
53.4
|
1.0
|
|
Calcium binding site 3 out
of 30 in 1yo8
Go back to
Calcium Binding Sites List in 1yo8
Calcium binding site 3 out
of 30 in the Structure of the C-Terminal Domain of Human Thrombospondin-2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of the C-Terminal Domain of Human Thrombospondin-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1184
b:74.0
occ:1.00
|
OD1
|
A:ASP926
|
2.1
|
70.2
|
1.0
|
O
|
A:ARG928
|
2.4
|
68.5
|
1.0
|
OD1
|
A:ASP930
|
2.4
|
69.0
|
1.0
|
OD1
|
A:ASP922
|
2.5
|
69.5
|
1.0
|
OD1
|
A:ASP924
|
2.5
|
77.1
|
1.0
|
CG
|
A:ASP926
|
3.1
|
69.2
|
1.0
|
CG
|
A:ASP924
|
3.4
|
76.2
|
1.0
|
OD2
|
A:ASP926
|
3.4
|
67.6
|
1.0
|
OD2
|
A:ASP924
|
3.4
|
76.6
|
1.0
|
C
|
A:ARG928
|
3.6
|
67.4
|
1.0
|
CG
|
A:ASP930
|
3.6
|
68.8
|
1.0
|
CG
|
A:ASP922
|
3.6
|
70.7
|
1.0
|
N
|
A:ASP930
|
3.8
|
66.5
|
1.0
|
CA
|
A:ASP930
|
3.9
|
66.4
|
1.0
|
C
|
A:GLY929
|
4.0
|
66.3
|
1.0
|
CA
|
A:ASP922
|
4.2
|
71.5
|
1.0
|
CB
|
A:ASP930
|
4.3
|
67.5
|
1.0
|
CB
|
A:ASP926
|
4.3
|
70.8
|
1.0
|
O
|
A:GLY929
|
4.3
|
66.1
|
1.0
|
CB
|
A:ASP922
|
4.3
|
71.2
|
1.0
|
CA
|
A:ARG928
|
4.4
|
67.1
|
1.0
|
CB
|
A:ARG928
|
4.4
|
66.5
|
1.0
|
N
|
A:ARG928
|
4.4
|
67.9
|
1.0
|
N
|
A:ASP926
|
4.4
|
72.6
|
1.0
|
OD2
|
A:ASP922
|
4.4
|
70.6
|
1.0
|
OD2
|
A:ASP930
|
4.5
|
69.1
|
1.0
|
N
|
A:GLY929
|
4.5
|
66.5
|
1.0
|
CA
|
A:GLY929
|
4.6
|
66.5
|
1.0
|
C
|
A:ASP922
|
4.7
|
72.8
|
1.0
|
N
|
A:LEU923
|
4.8
|
73.8
|
1.0
|
CA
|
A:ASP926
|
4.8
|
71.3
|
1.0
|
N
|
A:ASP924
|
4.8
|
76.2
|
1.0
|
CB
|
A:ASP924
|
4.8
|
76.5
|
1.0
|
|
Calcium binding site 4 out
of 30 in 1yo8
Go back to
Calcium Binding Sites List in 1yo8
Calcium binding site 4 out
of 30 in the Structure of the C-Terminal Domain of Human Thrombospondin-2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of the C-Terminal Domain of Human Thrombospondin-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1185
b:57.8
occ:1.00
|
OD1
|
A:ASP901
|
2.2
|
60.3
|
1.0
|
OD1
|
A:ASP903
|
2.3
|
63.4
|
1.0
|
OD2
|
A:ASP910
|
2.3
|
64.2
|
1.0
|
O
|
A:HOH1268
|
2.4
|
54.4
|
1.0
|
O
|
A:VAL905
|
2.4
|
65.3
|
1.0
|
OD1
|
A:ASP899
|
2.5
|
62.2
|
1.0
|
CG
|
A:ASP901
|
3.3
|
59.7
|
1.0
|
CG
|
A:ASP903
|
3.3
|
62.5
|
1.0
|
CG
|
A:ASP910
|
3.4
|
65.2
|
1.0
|
C
|
A:VAL905
|
3.6
|
66.0
|
1.0
|
OD2
|
A:ASP901
|
3.6
|
60.9
|
1.0
|
CG
|
A:ASP899
|
3.7
|
62.2
|
1.0
|
OD2
|
A:ASP903
|
3.7
|
60.6
|
1.0
|
CB
|
A:ASP910
|
4.1
|
65.9
|
1.0
|
N
|
A:ASP903
|
4.2
|
62.0
|
1.0
|
CA
|
A:CA1186
|
4.2
|
58.4
|
1.0
|
O
|
A:ARG913
|
4.2
|
59.6
|
1.0
|
N
|
A:ASP901
|
4.2
|
58.3
|
1.0
|
OD2
|
A:ASP899
|
4.4
|
63.5
|
1.0
|
N
|
A:VAL905
|
4.4
|
66.2
|
1.0
|
CA
|
A:VAL905
|
4.4
|
66.2
|
1.0
|
CA
|
A:ASP899
|
4.4
|
61.5
|
1.0
|
N
|
A:ASP900
|
4.4
|
59.1
|
1.0
|
OD1
|
A:ASP910
|
4.4
|
65.9
|
1.0
|
C
|
A:PRO906
|
4.5
|
66.2
|
1.0
|
CB
|
A:ASP903
|
4.5
|
62.7
|
1.0
|
C
|
A:ASP899
|
4.6
|
60.6
|
1.0
|
N
|
A:PRO906
|
4.6
|
66.7
|
1.0
|
CB
|
A:ASP901
|
4.6
|
58.8
|
1.0
|
OD1
|
A:ASP907
|
4.6
|
64.4
|
1.0
|
N
|
A:ASN902
|
4.6
|
59.9
|
1.0
|
CB
|
A:VAL905
|
4.6
|
65.9
|
1.0
|
CB
|
A:ASP899
|
4.6
|
62.4
|
1.0
|
CA
|
A:PRO906
|
4.7
|
66.5
|
1.0
|
CA
|
A:ASP903
|
4.7
|
63.3
|
1.0
|
O
|
A:PRO906
|
4.7
|
66.2
|
1.0
|
N
|
A:ASP907
|
4.7
|
66.1
|
1.0
|
CA
|
A:ASP901
|
4.8
|
58.7
|
1.0
|
C
|
A:ASP903
|
4.9
|
64.4
|
1.0
|
N
|
A:GLY904
|
4.9
|
64.8
|
1.0
|
C
|
A:ASP901
|
4.9
|
59.6
|
1.0
|
C
|
A:ARG913
|
5.0
|
60.0
|
1.0
|
|
Calcium binding site 5 out
of 30 in 1yo8
Go back to
Calcium Binding Sites List in 1yo8
Calcium binding site 5 out
of 30 in the Structure of the C-Terminal Domain of Human Thrombospondin-2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of the C-Terminal Domain of Human Thrombospondin-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1186
b:58.4
occ:1.00
|
OD2
|
A:ASP903
|
2.2
|
60.6
|
1.0
|
O
|
A:CYS912
|
2.3
|
61.5
|
1.0
|
OD1
|
A:ASN917
|
2.3
|
62.8
|
1.0
|
OD2
|
A:ASP901
|
2.4
|
60.9
|
1.0
|
O
|
A:VAL915
|
2.4
|
62.5
|
1.0
|
OD1
|
A:ASP910
|
2.6
|
65.9
|
1.0
|
OD2
|
A:ASP910
|
2.6
|
64.2
|
1.0
|
CG
|
A:ASP910
|
3.0
|
65.2
|
1.0
|
C
|
A:CYS912
|
3.3
|
61.3
|
1.0
|
CG
|
A:ASP903
|
3.3
|
62.5
|
1.0
|
CG
|
A:ASP901
|
3.5
|
59.7
|
1.0
|
C
|
A:VAL915
|
3.5
|
62.1
|
1.0
|
CG
|
A:ASN917
|
3.5
|
63.8
|
1.0
|
N
|
A:ASN917
|
3.6
|
65.8
|
1.0
|
OD1
|
A:ASP903
|
3.8
|
63.4
|
1.0
|
CB
|
A:CYS912
|
3.8
|
61.9
|
1.0
|
OD1
|
A:ASP901
|
3.9
|
60.3
|
1.0
|
NE2
|
A:GLN920
|
4.0
|
66.9
|
1.0
|
CA
|
A:CYS912
|
4.0
|
61.8
|
1.0
|
CA
|
A:CA1185
|
4.2
|
57.8
|
1.0
|
C
|
A:PHE916
|
4.2
|
65.3
|
1.0
|
N
|
A:CYS912
|
4.2
|
62.4
|
1.0
|
N
|
A:PHE916
|
4.3
|
62.8
|
1.0
|
CA
|
A:PHE916
|
4.3
|
64.2
|
1.0
|
N
|
A:VAL915
|
4.3
|
60.7
|
1.0
|
N
|
A:ARG913
|
4.3
|
60.6
|
1.0
|
CA
|
A:ASN917
|
4.4
|
66.3
|
1.0
|
ND2
|
A:ASN917
|
4.4
|
62.7
|
1.0
|
C
|
A:ARG913
|
4.4
|
60.0
|
1.0
|
CB
|
A:ASN917
|
4.5
|
65.8
|
1.0
|
CB
|
A:ASP910
|
4.5
|
65.9
|
1.0
|
CA
|
A:VAL915
|
4.5
|
61.1
|
1.0
|
O
|
A:ARG913
|
4.5
|
59.6
|
1.0
|
CA
|
A:ARG913
|
4.5
|
60.6
|
1.0
|
CB
|
A:ASP903
|
4.6
|
62.7
|
1.0
|
O
|
A:ASN917
|
4.6
|
67.0
|
1.0
|
C
|
A:ASN917
|
4.7
|
67.2
|
1.0
|
CB
|
A:ASP901
|
4.8
|
58.8
|
1.0
|
N
|
A:LEU914
|
4.9
|
59.6
|
1.0
|
|
Calcium binding site 6 out
of 30 in 1yo8
Go back to
Calcium Binding Sites List in 1yo8
Calcium binding site 6 out
of 30 in the Structure of the C-Terminal Domain of Human Thrombospondin-2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of the C-Terminal Domain of Human Thrombospondin-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1187
b:70.1
occ:1.00
|
OD2
|
A:ASP897
|
2.2
|
60.0
|
1.0
|
O
|
A:ASP899
|
2.4
|
61.2
|
1.0
|
OD1
|
A:ASN902
|
2.5
|
59.0
|
1.0
|
OD2
|
A:ASP890
|
2.5
|
61.1
|
1.0
|
OD1
|
A:ASP897
|
2.6
|
61.9
|
1.0
|
OD2
|
A:ASP888
|
2.6
|
58.4
|
1.0
|
CG
|
A:ASP897
|
2.7
|
61.2
|
1.0
|
O
|
A:HOH1235
|
2.9
|
48.4
|
1.0
|
CG
|
A:ASN902
|
3.4
|
58.5
|
1.0
|
C
|
A:ASP899
|
3.4
|
60.6
|
1.0
|
CG
|
A:ASP890
|
3.7
|
62.0
|
1.0
|
CG
|
A:ASP888
|
3.8
|
58.5
|
1.0
|
ND2
|
A:ASN902
|
3.9
|
55.3
|
1.0
|
CA
|
A:CA1188
|
3.9
|
55.9
|
1.0
|
CB
|
A:ASP899
|
4.0
|
62.4
|
1.0
|
OD1
|
A:ASP890
|
4.1
|
61.5
|
1.0
|
CA
|
A:ASP899
|
4.2
|
61.5
|
1.0
|
CB
|
A:ASP897
|
4.2
|
61.5
|
1.0
|
OD1
|
A:ASP888
|
4.2
|
58.0
|
1.0
|
N
|
A:ASP899
|
4.3
|
61.8
|
1.0
|
N
|
A:ASP900
|
4.4
|
59.1
|
1.0
|
N
|
A:ASN902
|
4.5
|
59.9
|
1.0
|
CA
|
A:ASP900
|
4.6
|
58.2
|
1.0
|
CB
|
A:ASN902
|
4.6
|
59.6
|
1.0
|
CA
|
A:ASN902
|
4.7
|
60.5
|
1.0
|
CG
|
A:ASP899
|
4.8
|
62.2
|
1.0
|
C
|
A:ASP900
|
4.8
|
58.0
|
1.0
|
CB
|
A:ASP890
|
5.0
|
62.0
|
1.0
|
OE1
|
A:GLN892
|
5.0
|
69.9
|
1.0
|
CB
|
A:ASP888
|
5.0
|
59.3
|
1.0
|
|
Calcium binding site 7 out
of 30 in 1yo8
Go back to
Calcium Binding Sites List in 1yo8
Calcium binding site 7 out
of 30 in the Structure of the C-Terminal Domain of Human Thrombospondin-2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of the C-Terminal Domain of Human Thrombospondin-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1188
b:55.9
occ:1.00
|
O
|
A:GLN892
|
2.2
|
57.9
|
1.0
|
OD1
|
A:ASP890
|
2.4
|
61.5
|
1.0
|
OD2
|
A:ASP897
|
2.4
|
60.0
|
1.0
|
OD1
|
A:ASP888
|
2.4
|
58.0
|
1.0
|
OD1
|
A:ASP886
|
2.5
|
59.5
|
1.0
|
CG
|
A:ASP888
|
3.2
|
58.5
|
1.0
|
OD2
|
A:ASP888
|
3.2
|
58.4
|
1.0
|
CG
|
A:ASP890
|
3.2
|
62.0
|
1.0
|
C
|
A:GLN892
|
3.3
|
58.8
|
1.0
|
OD2
|
A:ASP890
|
3.4
|
61.1
|
1.0
|
CG
|
A:ASP897
|
3.4
|
61.2
|
1.0
|
CG
|
A:ASP886
|
3.6
|
57.9
|
1.0
|
CB
|
A:ASP897
|
3.8
|
61.5
|
1.0
|
CA
|
A:CA1187
|
3.9
|
70.1
|
1.0
|
CA
|
A:GLN892
|
4.0
|
60.1
|
1.0
|
N
|
A:GLN892
|
4.1
|
60.1
|
1.0
|
CB
|
A:GLN892
|
4.2
|
61.0
|
1.0
|
N
|
A:ASP890
|
4.3
|
61.6
|
1.0
|
OD2
|
A:ASP886
|
4.3
|
59.8
|
1.0
|
N
|
A:GLY893
|
4.4
|
58.0
|
1.0
|
CB
|
A:ASP890
|
4.5
|
62.0
|
1.0
|
C
|
A:GLY893
|
4.5
|
57.3
|
1.0
|
OD1
|
A:ASP897
|
4.5
|
61.9
|
1.0
|
N
|
A:ASP894
|
4.6
|
56.5
|
1.0
|
CB
|
A:ASP888
|
4.6
|
59.3
|
1.0
|
CA
|
A:ASP886
|
4.6
|
55.0
|
1.0
|
N
|
A:ASP888
|
4.7
|
58.0
|
1.0
|
CB
|
A:ASP886
|
4.7
|
54.8
|
1.0
|
CA
|
A:GLY893
|
4.7
|
57.2
|
1.0
|
O
|
A:ASP900
|
4.7
|
57.8
|
1.0
|
OD1
|
A:ASP894
|
4.7
|
55.4
|
1.0
|
CA
|
A:ASP890
|
4.7
|
61.9
|
1.0
|
N
|
A:GLY891
|
4.7
|
60.7
|
1.0
|
C
|
A:ASP886
|
4.8
|
55.2
|
1.0
|
N
|
A:ARG889
|
4.8
|
60.0
|
1.0
|
O
|
A:GLY893
|
4.8
|
58.0
|
1.0
|
C
|
A:ASP890
|
4.9
|
62.0
|
1.0
|
CA
|
A:ASP900
|
4.9
|
58.2
|
1.0
|
O
|
A:ASP899
|
5.0
|
61.2
|
1.0
|
CA
|
A:ASP888
|
5.0
|
59.1
|
1.0
|
|
Calcium binding site 8 out
of 30 in 1yo8
Go back to
Calcium Binding Sites List in 1yo8
Calcium binding site 8 out
of 30 in the Structure of the C-Terminal Domain of Human Thrombospondin-2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure of the C-Terminal Domain of Human Thrombospondin-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1189
b:61.5
occ:1.00
|
OD2
|
A:ASP907
|
2.0
|
63.1
|
1.0
|
O
|
A:ASP897
|
2.2
|
62.0
|
1.0
|
O
|
A:ASP894
|
2.2
|
58.6
|
1.0
|
O
|
A:HOH1226
|
2.3
|
45.1
|
1.0
|
OD1
|
A:ASP900
|
2.6
|
56.9
|
1.0
|
OD2
|
A:ASP900
|
2.8
|
56.8
|
1.0
|
O
|
A:HOH1249
|
2.9
|
49.6
|
1.0
|
CG
|
A:ASP900
|
3.0
|
57.6
|
1.0
|
CG
|
A:ASP907
|
3.3
|
64.6
|
1.0
|
C
|
A:ASP894
|
3.3
|
58.1
|
1.0
|
C
|
A:ASP897
|
3.4
|
62.5
|
1.0
|
OD1
|
A:ASP907
|
4.0
|
64.4
|
1.0
|
CA
|
A:ASP894
|
4.0
|
57.0
|
1.0
|
N
|
A:ASP897
|
4.2
|
62.8
|
1.0
|
CA
|
A:ASP897
|
4.3
|
62.4
|
1.0
|
N
|
A:PRO898
|
4.3
|
63.1
|
1.0
|
CB
|
A:ASP907
|
4.3
|
65.5
|
1.0
|
CA
|
A:PRO898
|
4.4
|
63.3
|
1.0
|
N
|
A:ALA895
|
4.4
|
58.3
|
1.0
|
CB
|
A:ASP900
|
4.5
|
57.9
|
1.0
|
CB
|
A:ASP894
|
4.6
|
56.0
|
1.0
|
C
|
A:ALA895
|
4.7
|
61.0
|
1.0
|
CB
|
A:ASP897
|
4.7
|
61.5
|
1.0
|
C
|
A:PRO898
|
4.7
|
62.8
|
1.0
|
CA
|
A:ALA895
|
4.7
|
59.6
|
1.0
|
N
|
A:ASP899
|
4.8
|
61.8
|
1.0
|
O
|
A:ALA895
|
4.8
|
62.1
|
1.0
|
N
|
A:ASP900
|
4.9
|
59.1
|
1.0
|
N
|
A:CYS896
|
5.0
|
61.7
|
1.0
|
|
Calcium binding site 9 out
of 30 in 1yo8
Go back to
Calcium Binding Sites List in 1yo8
Calcium binding site 9 out
of 30 in the Structure of the C-Terminal Domain of Human Thrombospondin-2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Structure of the C-Terminal Domain of Human Thrombospondin-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1190
b:63.2
occ:1.00
|
OD2
|
A:ASP867
|
2.2
|
46.5
|
1.0
|
O
|
A:ILE879
|
2.2
|
56.0
|
1.0
|
OD2
|
A:ASP865
|
2.3
|
59.6
|
1.0
|
O
|
A:CYS876
|
2.4
|
61.0
|
1.0
|
OD2
|
A:ASP874
|
2.5
|
55.2
|
1.0
|
OD1
|
A:ASN881
|
2.5
|
51.9
|
1.0
|
OD1
|
A:ASP874
|
2.7
|
57.8
|
1.0
|
CG
|
A:ASP874
|
3.0
|
57.6
|
1.0
|
C
|
A:ILE879
|
3.2
|
57.2
|
1.0
|
CG
|
A:ASP867
|
3.4
|
48.6
|
1.0
|
N
|
A:ASN881
|
3.4
|
50.9
|
1.0
|
CG
|
A:ASP865
|
3.4
|
57.7
|
1.0
|
C
|
A:CYS876
|
3.5
|
61.3
|
1.0
|
CG
|
A:ASN881
|
3.7
|
50.2
|
1.0
|
CA
|
A:SER880
|
3.7
|
53.9
|
1.0
|
OD1
|
A:ASP865
|
3.7
|
57.3
|
1.0
|
C
|
A:SER880
|
3.8
|
52.5
|
1.0
|
N
|
A:SER880
|
3.9
|
55.9
|
1.0
|
OD1
|
A:ASP867
|
3.9
|
46.9
|
1.0
|
CB
|
A:CYS876
|
4.0
|
61.3
|
1.0
|
CA
|
A:CA1191
|
4.2
|
53.1
|
1.0
|
CA
|
A:CYS876
|
4.2
|
61.3
|
1.0
|
NE2
|
A:GLN884
|
4.2
|
48.8
|
1.0
|
N
|
A:ILE879
|
4.2
|
60.6
|
1.0
|
CA
|
A:ASN881
|
4.4
|
49.9
|
1.0
|
CA
|
A:ILE879
|
4.4
|
58.9
|
1.0
|
CB
|
A:ASN881
|
4.4
|
50.6
|
1.0
|
N
|
A:PRO877
|
4.5
|
62.0
|
1.0
|
N
|
A:CYS876
|
4.5
|
59.9
|
1.0
|
C
|
A:PRO877
|
4.5
|
62.0
|
1.0
|
CB
|
A:ASP874
|
4.5
|
57.4
|
1.0
|
CB
|
A:ASP867
|
4.5
|
47.8
|
1.0
|
CA
|
A:PRO877
|
4.6
|
61.9
|
1.0
|
ND2
|
A:ASN881
|
4.7
|
49.2
|
1.0
|
O
|
A:PRO877
|
4.7
|
61.8
|
1.0
|
CB
|
A:ASP865
|
4.7
|
57.0
|
1.0
|
N
|
A:TYR878
|
4.7
|
62.5
|
1.0
|
O
|
A:SER880
|
4.8
|
52.0
|
1.0
|
C
|
A:ASN881
|
4.8
|
49.3
|
1.0
|
O
|
A:ASN881
|
4.9
|
49.4
|
1.0
|
O
|
A:HOH1325
|
5.0
|
75.0
|
1.0
|
|
Calcium binding site 10 out
of 30 in 1yo8
Go back to
Calcium Binding Sites List in 1yo8
Calcium binding site 10 out
of 30 in the Structure of the C-Terminal Domain of Human Thrombospondin-2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Structure of the C-Terminal Domain of Human Thrombospondin-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1191
b:53.1
occ:1.00
|
OD1
|
A:ASP863
|
2.0
|
58.5
|
1.0
|
O
|
A:HIS869
|
2.2
|
50.0
|
1.0
|
OD1
|
A:ASP865
|
2.3
|
57.3
|
1.0
|
O
|
A:HOH1325
|
2.3
|
75.0
|
1.0
|
OD1
|
A:ASP867
|
2.4
|
46.9
|
1.0
|
OD2
|
A:ASP874
|
2.4
|
55.2
|
1.0
|
CG
|
A:ASP863
|
3.3
|
57.2
|
1.0
|
CG
|
A:ASP867
|
3.3
|
48.6
|
1.0
|
CG
|
A:ASP865
|
3.4
|
57.7
|
1.0
|
C
|
A:HIS869
|
3.4
|
50.1
|
1.0
|
CG
|
A:ASP874
|
3.5
|
57.6
|
1.0
|
OD2
|
A:ASP867
|
3.6
|
46.5
|
1.0
|
OD2
|
A:ASP865
|
3.7
|
59.6
|
1.0
|
N
|
A:HIS869
|
3.9
|
48.6
|
1.0
|
OD2
|
A:ASP863
|
4.0
|
54.0
|
1.0
|
CB
|
A:ASP874
|
4.1
|
57.4
|
1.0
|
CA
|
A:HIS869
|
4.1
|
49.4
|
1.0
|
CA
|
A:CA1190
|
4.2
|
63.2
|
1.0
|
CB
|
A:ASP863
|
4.2
|
57.7
|
1.0
|
N
|
A:ASP867
|
4.3
|
48.5
|
1.0
|
CB
|
A:HIS869
|
4.4
|
49.3
|
1.0
|
CA
|
A:ASP863
|
4.4
|
59.2
|
1.0
|
N
|
A:ASP865
|
4.4
|
57.8
|
1.0
|
N
|
A:GLN870
|
4.4
|
51.0
|
1.0
|
C
|
A:GLN870
|
4.4
|
54.3
|
1.0
|
O
|
A:PRO877
|
4.5
|
61.8
|
1.0
|
OD1
|
A:ASP874
|
4.5
|
57.8
|
1.0
|
CA
|
A:GLN870
|
4.6
|
52.6
|
1.0
|
O
|
A:GLN870
|
4.6
|
54.8
|
1.0
|
N
|
A:GLY868
|
4.6
|
48.2
|
1.0
|
C
|
A:ASP863
|
4.6
|
59.5
|
1.0
|
CB
|
A:ASP867
|
4.6
|
47.8
|
1.0
|
CB
|
A:ASP865
|
4.6
|
57.0
|
1.0
|
N
|
A:ASP866
|
4.7
|
53.4
|
1.0
|
N
|
A:ASN871
|
4.8
|
56.1
|
1.0
|
OD1
|
A:ASN871
|
4.8
|
59.0
|
1.0
|
CA
|
A:ASP867
|
4.8
|
47.8
|
1.0
|
CA
|
A:ASP865
|
4.8
|
56.5
|
1.0
|
N
|
A:ILE864
|
4.9
|
59.8
|
1.0
|
C
|
A:ASP865
|
4.9
|
54.5
|
1.0
|
C
|
A:ASP867
|
4.9
|
47.6
|
1.0
|
O
|
A:ASP863
|
5.0
|
59.4
|
1.0
|
|
Reference:
C.B.Carlson,
D.A.Bernstein,
D.S.Annis,
T.M.Misenheimer,
B.L.Hannah,
D.F.Mosher,
J.L.Keck.
Structure of the Calcium-Rich Signature Domain of Human Thrombospondin-2 Nat.Struct.Mol.Biol. V. 12 910 2005.
ISSN: ISSN 1545-9993
PubMed: 16186819
DOI: 10.1038/NSMB997
Page generated: Fri Jul 12 08:07:58 2024
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